[Chimera-users] problems in opening PDB file

Marco Sette sette at uniroma2.it
Tue Mar 24 08:34:03 PDT 2020

Dear Laura,

maybe you can have a look at your pdb file by using a text editor to 
check if the pdb contains some unusual portion (like missing residues). 
As far I know Chimera tries to reconstruct missing residues but 
sometimes there could be something wrong.

Best regards


Il 24/03/2020 10:05, Laura Rotilio ha scritto:
> Goodmorning,
> I'm writing because I'm trying to open my pdb file but this error came 
> out "Attempt to form loop bond".
> I tried to have a look at the _init_.py file in the line 1109 and I 
> found this message:
> molList = pdbio.readPDBfile(file, errOut=errLog)
> I can't understand this message and I don't know how to eventually 
> modify my pdb file in order to be able to open it.
> Thanks in advance for helping me,
> Laura Rotilio
> -- 
> Laura Rotilio, Ph.D. Student
> *Structural Biology Lab., Prof. A. Mattevi*
> Dept. Biology and Biotechnology "L. Spallanzani"
> University of Pavia
> Via Ferrata 9, 27100 Pavia
> Italy
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534
> Fax +39-0382-528496 <tel:%2B39-0382-528496>
> Web www.unipv.it/biocry <http://www.unipv.it/biocry>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200324/b24f2ba0/attachment.html>

More information about the Chimera-users mailing list